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- EMDB-46768: azoRhuA-bCDRhuA co-assembled nanotubes, 11-start -

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Basic information

Entry
Database: EMDB / ID: EMD-46768
TitleazoRhuA-bCDRhuA co-assembled nanotubes, 11-start
Map dataazoRhuA-bCDRhuA co-assembled nanotube, 11-start
Sample
  • Complex: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
    • Protein or peptide: L-rhamnulose-1-phosphate aldolase
KeywordsAssembly / LYASE
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsZhang Z / Sonani RR / Wang F / Egelman EH / Tezcan FA
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Chem / Year: 2025
Title: Design of light- and chemically responsive protein assemblies through host-guest interactions.
Authors: Zhiyin Zhang / Huat T Chiang / Ying Xia / Nicole Avakyan / Ravi R Sonani / Fengbin Wang / Edward H Egelman / James J De Yoreo / Lilo D Pozzo / F Akif Tezcan /
Abstract: Host-guest interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse ...Host-guest interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse stimuli. Here we have set out to exploit these advantages of host-guest chemistry in the design of dynamic protein assemblies, using a symmetric protein, RhuA, as a building block. We show that RhuA variant individually modified with β-cyclodextrin (βCD) (host) or azobenzene (guest) functionalities can specifically pair with each other to form highly ordered 1- and 2-D assemblies. Association and dissociation RhuA-RhuA assemblies can be controlled by UV and visible light as well as by small-molecule modulators of βCD-azobenzene interactions. Kinetics analyses reveal that RhuA-RhuA nanotubes assemble without a nucleation barrier, a highly unusual occurrence for helical supramolecular systems. Taken together, our findings provide a compelling example for achieving complex structural and dynamic outcomes in protein assembly through simple chemical design.
History
DepositionAug 27, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46768.png

Downloads & links

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Map

FileDownload / File: emd_46768.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationazoRhuA-bCDRhuA co-assembled nanotube, 11-start
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 480 pix.
= 825.6 Å		1.72 Å/pix.
x 480 pix.
= 825.6 Å		1.72 Å/pix.
x 480 pix.
= 825.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63
Minimum - Maximum-0.25997335 - 1.4884341
Average (Standard dev.)0.03457295 (±0.14163888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 825.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: azoRhuA-bCDRhuA co-assembled nanotube, 11-start, half map A

Fileemd_46768_half_map_1.map
AnnotationazoRhuA-bCDRhuA co-assembled nanotube, 11-start, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: azoRhuA-bCDRhuA co-assembled nanotube, 11-start, half map B

Fileemd_46768_half_map_2.map
AnnotationazoRhuA-bCDRhuA co-assembled nanotube, 11-start, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of azobenzene and beta-cyclodextrin modified RhuA

EntireName: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
Components
  • Complex: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
    • Protein or peptide: L-rhamnulose-1-phosphate aldolase

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Supramolecule #1: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA

SupramoleculeName: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: L-rhamnulose-1-phosphate aldolase

MacromoleculeName: L-rhamnulose-1-phosphate aldolase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSCGA GYHILWGLTN EAVPTSELPA HFLSHSERIK ATNGKDRVIM HCHATNLIAL TYVLENDTAV FTRQLWEGST ...String:
MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSCGA GYHILWGLTN EAVPTSELPA HFLSHSERIK ATNGKDRVIM HCHATNLIAL TYVLENDTAV FTRQLWEGST ECLVVFPDGV GILPWMVPGT DAIGQATAQE MQKHSLVLWP FHGVFGSGPT LDETFGLIDT AEKSAQVLVK VYSMGGMKQT ISREELIALG KRFGVTPLAS ALAL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 132.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 245152
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1gt7

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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